[English] 日本語
Yorodumi
- PDB-8rpb: Structure of S79 Fab in complex with IgV domain of human PD-L1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rpb
TitleStructure of S79 Fab in complex with IgV domain of human PD-L1
Components
  • Programmed cell death 1 ligand 1
  • heavy chain of S79 fab
  • light chain of S79 fab
KeywordsIMMUNE SYSTEM / Fab
Function / homology
Function and homology information


positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsSvensson, A. / Kelpsas, V. / Laursen, M. / Rose, N.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Mabs / Year: 2024
Title: Structural analysis of light chain-driven bispecific antibodies targeting CD47 and PD-L1.
Authors: Malinge, P. / Chauchet, X. / Bourguignon, J. / Bosson, N. / Calloud, S. / Bautzova, T. / Borlet, M. / Laursen, M. / Kelpsas, V. / Rose, N. / Gueneau, F. / Ravn, U. / Magistrelli, G. / Fischer, N.
History
DepositionJan 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: heavy chain of S79 fab
L: light chain of S79 fab
P: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,61713
Polymers60,7293
Non-polymers88810
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-110 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.852, 185.852, 110.237
Angle α, β, γ (deg.)90, 90, 120
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11H-306-

SO4

21H-306-

SO4

-
Components

-
Protein , 1 types, 1 molecules P

#3: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14335.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7

-
Antibody , 2 types, 2 molecules HL

#1: Antibody heavy chain of S79 fab


Mass: 23468.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody light chain of S79 fab


Mass: 22925.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 27 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.0, 1.6M Li2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.79→48.24 Å / Num. obs: 28276 / % possible obs: 99.7 % / Redundancy: 24 % / CC1/2: 0.995 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.043 / Net I/σ(I): 11.8
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 23.9 % / Rmerge(I) obs: 3.089 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3987 / CC1/2: 0.622 / Rpim(I) all: 0.637 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.794→48.24 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.383 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1385 -RANDOM
Rwork0.2289 ---
obs0.23 28249 99.8 %-
Displacement parametersBiso mean: 119.06 Å2
Baniso -1Baniso -2Baniso -3
1--3.0203 Å20 Å20 Å2
2---3.0203 Å20 Å2
3---6.0406 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.794→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 49 17 4190
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074263HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965799HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1397SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes703HARMONIC5
X-RAY DIFFRACTIONt_it4263HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion558SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2908SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion16.79
LS refinement shellResolution: 2.794→2.81 Å
RfactorNum. reflection% reflection
Rfree0.3519 24 -
Rwork0.3414 --
obs--90.51 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.4416-0.0740.94852.05230.74042.6844-0.397-0.1112-0.3155-0.1112-0.03550.5856-0.31550.58560.4326-0.24570.1743-0.19320.1993-0.02560.1313-17.4374-74.7604-9.3984
26.8902-0.8761.30218.322.25085.0447-1.21151.5701-0.4341.57011.191-0.2982-0.434-0.29820.02050.02840.8038-0.36640.5367-0.5064-0.2772-40.2809-60.958412.792
311.6712-2.53931.62826.8222-2.34298.8733-0.6184-0.6389-0.7085-0.6389-0.27012.4728-0.70852.47280.8885-0.7768-0.1817-0.04741.11640.8076-0.37122.3222-71.1313-29.0013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|1 - H|116 L|1 - L|113 }H1 - 116
2X-RAY DIFFRACTION1{ H|1 - H|116 L|1 - L|113 }L1 - 113
3X-RAY DIFFRACTION2{ H|117 - H|218 L|114 - L|215 }H117 - 218
4X-RAY DIFFRACTION2{ H|117 - H|218 L|114 - L|215 }L114 - 215
5X-RAY DIFFRACTION3{ P|* }P18 - 131

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more